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Open science

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Open science

  1. 1. Open Science
  2. 2. Why do governments fund scientific research?
  3. 3. NIH Mission•  foster fundamental creative discoveries, innovative research strategies, and their applications as a basis to advance significantly the Nations capacity to protect and improve health;•  develop, maintain, and renew scientific human and physical resources that will assure the Nations capability to prevent disease;•  expand the knowledge base in medical and associated sciences in order to enhance the Nations economic well-being and ensure a continued high return on the public investment in research; and•  exemplify and promote the highest level of scientific integrity, public accountability, and social responsibility in the conduct of science.
  4. 4. Examples of Open Science•  Open Access publishing•  Open Notebooks•  Prepublication Data Release•  Open Source software
  5. 5. Three aspects of open science•  Cost•  Restrictions•  Timing
  6. 6. Costs of publishing•  Peer review•  Formatting and editing•  Dissemination
  7. 7. Creative Commons Attribution LicenseCopyright: © Eisen et al. 2006. This is an open-access article distributedunder the terms of the Creative Commons Attribution License, which permitsunrestricted use, distribution, and reproduction in any medium, provided theoriginal work is properly cited.Goal: overcome access barriers and encourage creative uses.www.creativecommons.org
  8. 8. Translation Coursepacks Photocopying Deposit in databases No permission required for any reuseDownloadingdata Reproduction Text mining of figures Redistribution
  9. 9. Public Library of Science (PLoS) NIH)•  Started in 2000 by –  Harold Varmus (ex-head of –  Pat Brown (HHMI, Stanford) –  Michael Eisen (my brother)•  PLoSs first action was to circulate an open letter•  Letter “encouraged” scientific publishers to make the research literature available for distribution through free online public archives such as the US National Library of Medicines PubMed Central.
  10. 10. The LetterWe support the establishment of an online public library that wouldprovide the full contents of the published record of research andscholarly discourse in medicine and the life sciences in a freely accessible,fully searchable, interlinked form. Establishment of this public library wouldvastly increase the accessibility and utility of the scientific literature,enhance scientific productivity, and catalyze integration of the disparatecommunities of knowledge and ideas in biomedical sciences.We recognizethat the publishers of our scientific journals have a legitimate right to a fairfinancial return for their role in scientific communication. We believe,however, that the permanent, archival record of scientific research andideas should neither be owned nor controlled by publishers, but shouldbelong to the public and should be freely available through an internationalonline public library.To encourage the publishers of our journals to supportthis endeavor, we pledge that, beginning in September 2001, we willpublish in, edit or review for, and personally subscribe to only thosescholarly and scientific journals that have agreed to grantunrestricted free distribution rights to any and all original researchreports that they have published, through PubMed Central and similaronline public resources, within 6 months of their initial publication date.
  11. 11. The LetterWe support the establishment of an online public library that wouldprovide the full contents of the published record of research andscholarly discourse in medicine and the life sciences in a freely accessible,fully searchable, interlinked form. Establishment of this public library wouldvastly increase the accessibility and utility of the scientific literature,enhance scientific productivity, and catalyze integration of the disparatecommunities of knowledge and ideas in biomedical sciences.We recognizethat the publishers of our scientific journals have a legitimate right to a fairfinancial return for their role in scientific communication. We believe,however, that the permanent, archival record of scientific research andideas should neither be owned nor controlled by publishers, but shouldbelong to the public and should be freely available through an internationalonline public library.To encourage the publishers of our journals to supportthis endeavor, we pledge that, beginning in September 2001, we willpublish in, edit or review for, and personally subscribe to only thosescholarly and scientific journals that have agreed to grantunrestricted free distribution rights to any and all original researchreports that they have published, through PubMed Central and similaronline public resources, within 6 months of their initial publication date.
  12. 12. After the Letter (2003)•  > 25,000 people signed the letter•  Letter had some impact in moving some publishers to freer access•  Led to some increase in support for existing OA journals like those from Biomed Central•  Unfortunately, not enough impact•  So announced the launch of their own journals –  PLoS Biology –  PLoS Medicine
  13. 13. Data Release•  Represented TIGR at Feb 2003 meeting in Ft. Lauderdale on “Genome Sequencing Data Release Policies”•  Follow up to the “Bermuda Accord”•  Debate about how open to be with data•  Surprised to learn that NHGRI had supported a similar policy to TIGRs (see http://www.genome.gov/10506537)•  Sean Eddy gave a talk that convinced me that these restrictions we in direct conflict with the whole point of giving money to places to generate the data•  So I did what any scientist should do - some experiments
  14. 14. Open Data Experiment data •  Unrestricted access policy on Tetrahymena thermophila •  First time done at TIGR •  Many people published papers before we did •  But many more helped with our paper1 The Institute for Genomic Research, Rockville, Maryland, United States of America, 2 Department of Biology, York University, Toronto, Ontario, Canada, 3Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada, 4 Department of Biological Sciences, Marquette University, Milwaukee,Wisconsin, United States of America, 5 Razavi-Newman Center for Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, UnitedStates of America, 6 Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America, 7 Department ofBiology, Harvey Mudd College, Claremont, California, United States of America, 8 Department of Biology, University of Texas at San Antonio, San Antonio,Texas, United States of America, 9 Department of Electrical Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America, 10Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America, 11 Department of ComputerScience and Engineering, University of Washington, Seattle, Washington, United States of America, 12 Department of Cellular Biology, University of Georgia,Athens, Georgia, United States of America, 13 Department of Biological Sciences, University of Iowa, Iowa City, Iowa, United States of America, 14Department of Biology, University of Rochester, Rochester, New York, United States of America, 15 Canadian Institute for Advanced Research, Department ofBotany, University of British Columbia, Vancouver, British Columbia, Canada, 16 Department of Genetics, Stanford University, Stanford, California, UnitedStates of America, 17 Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, UnitedStates of America
  15. 15. Open Publishing Experiment •  Had published one paper in a BMC Open Access journal (Genome Biology) •  But not a high profile one •  We were working on a paper on the first Wolbachia genome •  Wolbachia are intracellular bacteria that target males for detrimental effects in some invertebrates •  Wolbachia also are mutualistic symbionts of filiarial nematodes •  Our paper was being recruited by Nature and Science •  We agreed to submit the paper to PLoS Biology
  16. 16. RhoGam•  Supplier –  RhoGAM should be administered within 72 hours of known or suspected exposure to Rh-positive red blood cells.•  Wikipedia –  It is given by intramuscular injection as part of modern routine antenatal care at about 28 weeks of pregnancy, and within 72 hours after childbirth.[5] It is also given after antenatal pathological events that are likely to cause a feto- maternal hemorrhage.[6]•  Question –  What happens if you do it even later?
  17. 17. You can purchase online access tothis article (and all its versions) for a24-hour period. Articles are US $ 29.95, with some exceptions whereprices may vary. Click "Buy Now" todisplay the price
  18. 18. Access Blocked - What Next?•  Bought lots of articles. –  Few were helpful. –  Note - can’t read before buying•  Tried to contact experts –  Wrote to authors if I could find email addresses. –  Got back some papers but many came weeks or months later. –  Called authors and others –  Time was of the essence•  Got friends to get some articles from libraries –  Hard to do at 3 AM sitting bedside at hospital•  Got more and more pissed off
  19. 19. Medical Guesswork•  Wife got Rhogam 9 days after blood exposure•  Other treatments (for clots, bleeding, infection, loss of amniotic fluid, etc,) became in part guesswork as well•  Common theme –  If you have a somewhat unusual situation –  Your doctors may not know all they need to know –  They are busy –  Need to take medical care into your own hands –  But frequently you can’t
  20. 20. Many Flavors ofAccessibility and OpennessCost Free $, $$, or $$$Timing of Immediate LaterfreeLocation Archives Journal siteReuse Unrestricted RestrictedCopyright Author JournalWho Journal Individualarchives
  21. 21. Green Open AccessCost Free $, $$, or $$$Timing of Immediate LaterfreeLocation Archives Journal siteReuse Unrestricted RestrictedCopyright Author JournalWho Journal Individualarchives
  22. 22. Gold Open AccessCost Free $, $$, or $$$Timing of Immediate LaterfreeLocation Archives Journal siteReuse Unrestricted RestrictedCopyright Author JournalWho Journal Individualarchives Based on the Bethesda Principles, April 2003
  23. 23. Component #1: Free Access
  24. 24. “Ten million American adults look online for health information on a typical day.”From the Pew Research CenterSeeking Health On-line 2006 studyhttp://pewresearch.org/reports/?ReportID=65
  25. 25. Everyone should have access to research findings•  “It is not for either publishers or academics to decide who should, and who should not, be allowed to read scientific journal articles. We are encouraged by the growing interest in research findings shown by the public. It is in society’s interest that public understanding of science should increase. Increased public access to research findings should be encouraged by publishers, academics and Government alike” •  HoC S&T Committee Report, July 2004
  26. 26. The inspiration for Open Access is not a new idea“I want a poor student to have the same meansof indulging his learned curiosity,of following his rational pursuits,of consulting the same authorities,of fathoming the most intricate inquiryas the richest man in the kingdom…”Antonio Panizzi, 1836Principle Librarian of the British Museum
  27. 27. Component #2:Immediate Access
  28. 28. Timing of Access•  NIH and other guidelines now require access after six months•  Delay supposedly improves ability of journals to maintain subscriptions•  Immediate OA is the way science should work –  Public and others can get engaged when press coverage occurs –  Science happens rapidly –  Articles there whenever you look
  29. 29. Component #3: Archives
  30. 30. Component #4: License
  31. 31. Creative Commons Attribution LicenseCopyright: © Eisen et al. 2006. This is an open-access article distributedunder the terms of the Creative Commons Attribution License, which permitsunrestricted use, distribution, and reproduction in any medium, provided theoriginal work is properly cited.Goal: overcome access barriers and encourage creative uses.www.creativecommons.org
  32. 32. Translation Coursepacks Photocopying Deposit in databases No permission required for any reuseDownloadingdata Reproduction Text mining of figures Redistribution
  33. 33. Component #5: Copyright
  34. 34. Copyright Issues1.  Authors are the copyright holders until they transfer away their rights.2.  Transferring full copyright to a publisher gives the OA decision to the publisher.3.  Many journals will alter the standard contract when asked.4.  There’s no harm in asking.5.  Experts can help (e.g. author addenda). Slide based on one by Peter Suber
  35. 35. Component #6:Journal Handles Archiving
  36. 36. Self-archiving sluggishness•  “Of the authors who have not yet self- archived any articles, 71% remain unaware of the option.” –  Alma Swan and Sheridan Brown, Open access self-archiving: An author study –  http://cogprints.org/4385/ Slide based on one by Peter Suber
  37. 37. Part III: Benefits of Open Access
  38. 38. OA is about Freeing The Literature
  39. 39. You can purchase online access tothis article (and all its versions) for a24-hour period. Articles are US $ 29.95, with some exceptions whereprices may vary. Click "Buy Now" todisplay the price
  40. 40. You can purchase online access tothis article (and all its versions) for a24-hour period. Articles are US $ 29.95, with some exceptions whereprices may vary. Click "Buy Now" todisplay the price
  41. 41. Benefit #1:New mining
  42. 42. Document A network of literature
  43. 43. DocumentDatabase A network of literature and data
  44. 44. Jensen, Saric and Bork Nature Reviews GeneticsFeb 2006
  45. 45. Text mining and open access“So far, more that 90% of all biomedical literature mining hasbeen based on Medline, mainly because it is freely availablein a convenient format.”“…future methods should be able to extract information fromthe full text of papers…”“However, it is restricted access to the full text of papers…that is currently the greatest limitation…” Jensen, Saric and Bork Nature Reviews Genetics Feb 2006
  46. 46. Benefit #2:Education
  47. 47. Educational Benefits of OA•  No debate about “fair use”•  No need for password’s or logins for course web sites•  No lawyers have to be involved•  Material from OA publications can be repackaged for any purpose

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